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<h1>Input File Format</h1>

<p id="littleright">The inputfile is in a tab separated values format (i.e., the fields 
of the file are separated by the tabular character). The <em>first column</em>
is an arbitrary string for the name of the entity (gene, gene product, disease, pubmed article, etc.) and
the <em>second column</em> is one ontology term identifier (e.g., <tt>GO:0008150</tt>, <tt>DOID:123</tt>, <tt>MP:0000023</tt>).
If an entity is annotated to several ontology terms, each of the annotations is listed in a separate line. 
Ontology terms assigned to one entity can be taken from multiple OBO
  ontologies. The <em>third column</em> assigns the entities to a
  group and can be either 0 or 1. OntoSIML will compute the similarity
  between all entities in the first group and all entities in the
  second. To compute pairwise similarity between within one group of
  entities, entities must be listed twice in the input file, once in
  group 0 and once in group 1.</p>

<h2>Example Input File (single ontology, pairwise similarity)</h2>

<pre>
  NM_000014       GO:0008320      0
  NM_000014       GO:0017114      0
  NM_000015       GO:0004060      0
  NM_000017       GO:0004085      0
  NM_000014       GO:0008320      1
  NM_000014       GO:0017114      1
  NM_000015       GO:0004060      1
  NM_000017       GO:0004085      1
</pre>

<h2>Example Input File (mixed ontologies, pairwise similarity)</h2>

<pre>
  PMID:12345      DOID:52         0
  PMID:12345      GO:0008320      0
  PMID:12345      GO:0017114      0
  PMID:12345      CL:0000130      0
  PMID:54321      CL:0000130      0
  PMID:54321      CHEBI:0055591   0
  PMID:12345      DOID:52         1
  PMID:12345      GO:0008320      1
  PMID:12345      GO:0017114      1
  PMID:12345      CL:0000130      1
  PMID:54321      CL:0000130      1
  PMID:54321      CHEBI:0055591   1
</pre>

<h2>Example Input File (similarity between two groups)</h2>

<pre>
  OMIM:127100     MP:0009672      1
  OMIM:127100     MP:0009674      1
  OMIM:127100     MP:0009700      1
  OMIM:127100     MP:0009701      1
  OMIM:127100     MP:0009703      1
  MGI:1857242     MP:0000001      0
  MGI:1857242     MP:0000055      0
  MGI:1857242     MP:0000095      0
  MGI:1857242     MP:0000169      0
  MGI:1857411     MP:0005385      0
  MGI:1857411     MP:0005387      0
  MGI:1857411     MP:0005388      0
  MGI:97451       MP:0000463      0
  MGI:97451       MP:0000594      0
  MGI:97451       MP:0000631      0
  OMIM:100300     MP:0002170      1
  OMIM:100300     MP:0002171      1
  OMIM:100300     MP:0002191      1
  OMIM:100300     MP:0002199      1
  OMIM:100300     MP:0002221      1
  OMIM:100300     MP:0002339      1
</pre>

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